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Detailed information for vg0602322093:

Variant ID: vg0602322093 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 2322093
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:

ACGGAACAATGGTTGAGTGACACGGTCATCAACACTAGAAAGGAAAGTTGAAAAATTTCATAATAAGTTGAACATGGATAGCAAAATGCACACTCCACAC[G/A]
CAATACCTCTTCATCGGGCTCTCCATTTTCATCTAGTGCATCTTCTGTTTCCTCATCTTCAATGACCTGCATCCTTTTGAAAGCTTCCACAAGAGTCATG

Reverse complement sequence

CATGACTCTTGTGGAAGCTTTCAAAAGGATGCAGGTCATTGAAGATGAGGAAACAGAAGATGCACTAGATGAAAATGGAGAGCCCGATGAAGAGGTATTG[C/T]
GTGTGGAGTGTGCATTTTGCTATCCATGTTCAACTTATTATGAAATTTTTCAACTTTCCTTTCTAGTGTTGATGACCGTGTCACTCAACCATTGTTCCGT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	97.00%	1.80%	1.18%	0.00%	NA
All Indica	2759	95.00%	3.00%	1.92%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	83.40%	10.30%	6.39%	0.00%	NA
Indica II	465	98.50%	0.00%	1.51%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	96.10%	2.90%	1.02%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	0.00%	3.33%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0602322093	G -> A	LOC_Os06g05180.3	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:51.516; most accessible tissue: Zhenshan97 flower, score: 71.992	N	N	N	N
vg0602322093	G -> A	LOC_Os06g05180.4	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:51.516; most accessible tissue: Zhenshan97 flower, score: 71.992	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0602322093	NA	7.17E-07	Spikelet_length	Ind_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0602322093	NA	1.06E-09	mr1038	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0602322093	4.38E-06	2.84E-06	mr1386	Ind_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0602322093	NA	1.95E-09	mr1389	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0602322093	NA	1.41E-06	mr1740	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0602322093	NA	8.36E-09	mr1038_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0602322093	NA	2.38E-07	mr1092_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0602322093	NA	1.60E-07	mr1152_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0602322093	NA	2.94E-07	mr1389_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251